Starting phenix.real_space_refine (version: 1.21rc1) on Sat Oct 14 03:19:15 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4w_23668/10_2023/7m4w_23668_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4w_23668/10_2023/7m4w_23668.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4w_23668/10_2023/7m4w_23668_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4w_23668/10_2023/7m4w_23668_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4w_23668/10_2023/7m4w_23668_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4w_23668/10_2023/7m4w_23668.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4w_23668/10_2023/7m4w_23668.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4w_23668/10_2023/7m4w_23668_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m4w_23668/10_2023/7m4w_23668_updated.pdb" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.068 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 95 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4372 5.49 5 Mg 191 5.21 5 S 140 5.16 5 C 68830 2.51 5 N 25467 2.21 5 O 38919 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ASP 114": "OD1" <-> "OD2" Residue "C ASP 270": "OD1" <-> "OD2" Residue "D ASP 31": "OD1" <-> "OD2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D ASP 111": "OD1" <-> "OD2" Residue "D ASP 170": "OD1" <-> "OD2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "F ASP 94": "OD1" <-> "OD2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "F ASP 164": "OD1" <-> "OD2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 14": "OD1" <-> "OD2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 19": "OD1" <-> "OD2" Residue "I PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 5": "OE1" <-> "OE2" Residue "J ASP 9": "OD1" <-> "OD2" Residue "J ASP 12": "OD1" <-> "OD2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 116": "OE1" <-> "OE2" Residue "M GLU 32": "OE1" <-> "OE2" Residue "M GLU 89": "OE1" <-> "OE2" Residue "M PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O GLU 88": "OE1" <-> "OE2" Residue "P TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 91": "OD1" <-> "OD2" Residue "Q TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 23": "OE1" <-> "OE2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "V PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 83": "OE1" <-> "OE2" Residue "W PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 19": "OD1" <-> "OD2" Residue "Z GLU 24": "OE1" <-> "OE2" Residue "Z GLU 35": "OE1" <-> "OE2" Residue "b TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 31": "OE1" <-> "OE2" Residue "c GLU 105": "OE1" <-> "OE2" Residue "c ASP 112": "OD1" <-> "OD2" Residue "c TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 90": "OE1" <-> "OE2" Residue "d GLU 115": "OE1" <-> "OE2" Residue "e GLU 12": "OE1" <-> "OE2" Residue "e PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "h GLU 50": "OE1" <-> "OE2" Residue "h GLU 68": "OE1" <-> "OE2" Residue "i TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 14": "OD1" <-> "OD2" Residue "j ASP 75": "OD1" <-> "OD2" Residue "k PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ASP 54": "OD1" <-> "OD2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 10": "OE1" <-> "OE2" Residue "n GLU 40": "OE1" <-> "OE2" Residue "n PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 7": "OD1" <-> "OD2" Residue "o GLU 76": "OE1" <-> "OE2" Residue "o TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 22": "OD1" <-> "OD2" Residue "r TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 59": "OD1" <-> "OD2" Residue "u GLU 63": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 137923 Number of models: 1 Model: "" Number of chains: 76 Chain: "0" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 427 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "2" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "3" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 58566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2730, 58566 Classifications: {'RNA': 2730} Modifications used: {'rna2p': 3, 'rna2p_pur': 251, 'rna2p_pyr': 152, 'rna3p': 12, 'rna3p_pur': 1309, 'rna3p_pyr': 1003} Link IDs: {'rna2p': 405, 'rna3p': 2324} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 7, 'rna3p_pur': 58, 'rna3p_pyr': 48} Link IDs: {'rna2p': 8, 'rna3p': 106} Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2111 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1572 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain: "E" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1516 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1370 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1318 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 458 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "I" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1125 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1071 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "L" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1087 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 857 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "O" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "P" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "Q" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "S" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "T" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 766 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 585 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "W" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 632 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 486 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Y" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 455 Classifications: {'peptide': 57} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "Z" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 456 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain: "a" Number of atoms: 32782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32782 Classifications: {'RNA': 1528} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 110, 'rna2p_pyr': 91, 'rna3p': 8, 'rna3p_pur': 753, 'rna3p_pyr': 565} Link IDs: {'rna2p': 201, 'rna3p': 1326} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 5 Chain: "b" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "c" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "d" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1631 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain: "e" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "f" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "g" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1127 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain breaks: 1 Chain: "h" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 985 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "j" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 801 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "k" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Chain: "m" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "n" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 792 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 705 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "q" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "r" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "s" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 522 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 216 Unusual residues: {' MG': 136, 'YQM': 2} Classifications: {'undetermined': 138} Link IDs: {None: 137} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 92 Unusual residues: {' MG': 52, 'YQM': 1} Classifications: {'undetermined': 53} Link IDs: {None: 52} Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 597 Classifications: {'water': 597} Link IDs: {None: 596} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 156 Classifications: {'water': 156} Link IDs: {None: 155} Chain: "i" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "n" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "s" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1382 SG CYS 3 11 179.763 114.642 137.357 1.00 18.90 S ATOM 1398 SG CYS 3 14 178.613 116.160 140.723 1.00 18.99 S ATOM 1503 SG CYS 3 27 179.901 118.407 137.925 1.00 18.81 S Time building chain proxies: 50.91, per 1000 atoms: 0.37 Number of scatterers: 137923 At special positions: 0 Unit cell: (228.112, 245.92, 276.448, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 140 16.00 P 4372 15.00 Mg 191 11.99 F 3 9.00 O 38919 8.00 N 25467 7.00 C 68830 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 54.44 Conformation dependent library (CDL) restraints added in 5.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " Number of angles added : 3 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10118 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 171 helices and 69 sheets defined 39.5% alpha, 19.2% beta 1426 base pairs and 2119 stacking pairs defined. Time for finding SS restraints: 61.94 Creating SS restraints... Processing helix chain '0' and resid 22 through 27 Proline residue: 0 27 - end of helix Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.177A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 Processing helix chain '2' and resid 36 through 45 removed outlier: 3.730A pdb=" N ARG 2 44 " --> pdb=" O ILE 2 40 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N GLY 2 45 " --> pdb=" O ARG 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.324A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N SER 2 56 " --> pdb=" O SER 2 52 " (cutoff:3.500A) Proline residue: 2 62 - end of helix Processing helix chain 'C' and resid 10 through 15 removed outlier: 5.080A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.645A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 4.227A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.118A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 265 removed outlier: 4.943A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 265' Processing helix chain 'C' and resid 197 through 202 removed outlier: 3.540A pdb=" N ASN C 200 " --> pdb=" O ASN C 197 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ASN C 201 " --> pdb=" O GLN C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.595A pdb=" N VAL D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 62' Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.650A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.571A pdb=" N GLU D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.924A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 6.108A pdb=" N SER E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.536A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 162 removed outlier: 4.568A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.832A pdb=" N LEU E 179 " --> pdb=" O ASP E 175 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE E 180 " --> pdb=" O PRO E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'F' and resid 5 through 21 removed outlier: 4.273A pdb=" N ASN F 9 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ALA F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.708A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.987A pdb=" N GLY F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 5.104A pdb=" N ILE F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 142 through 147 removed outlier: 4.387A pdb=" N ILE F 146 " --> pdb=" O ASP F 142 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N ASP F 147 " --> pdb=" O PHE F 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 142 through 147' Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'G' and resid 2 through 8 Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 58 through 81 Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.794A pdb=" N TYR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 51 through 59 removed outlier: 3.869A pdb=" N GLU H 58 " --> pdb=" O LEU H 54 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 38 removed outlier: 3.874A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 88 through 96 Processing helix chain 'I' and resid 97 through 110 removed outlier: 3.592A pdb=" N MET I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 122 removed outlier: 3.579A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N MET I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 118 Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.791A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LYS K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 44' Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.727A pdb=" N LEU K 63 " --> pdb=" O ILE K 59 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 70 through 77 removed outlier: 3.750A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 88 removed outlier: 3.965A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N LYS K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL K 87 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLU K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 88' Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'L' and resid 43 through 59 Processing helix chain 'L' and resid 110 through 126 removed outlier: 3.690A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Proline residue: L 126 - end of helix Processing helix chain 'M' and resid 13 through 32 Processing helix chain 'M' and resid 38 through 57 removed outlier: 3.844A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.462A pdb=" N ASN M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 3.893A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLY M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) Proline residue: M 85 - end of helix Processing helix chain 'N' and resid 3 through 23 removed outlier: 4.381A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 85 Processing helix chain 'N' and resid 100 through 113 Processing helix chain 'O' and resid 5 through 16 removed outlier: 3.851A pdb=" N SER O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.608A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.224A pdb=" N SER O 107 " --> pdb=" O LEU O 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 100 through 107' Processing helix chain 'P' and resid 6 through 22 removed outlier: 3.575A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.923A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 87 Processing helix chain 'P' and resid 91 through 102 Processing helix chain 'P' and resid 103 through 118 Processing helix chain 'R' and resid 13 through 25 removed outlier: 3.967A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 41 through 61 removed outlier: 4.257A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 3.750A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LYS R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 70' Processing helix chain 'S' and resid 2 through 10 removed outlier: 4.409A pdb=" N LEU S 10 " --> pdb=" O ILE S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 26 Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.182A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ALA T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 64 through 69' Processing helix chain 'U' and resid 12 through 17 removed outlier: 5.259A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 Processing helix chain 'U' and resid 47 through 58 removed outlier: 3.696A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N ASN U 58 " --> pdb=" O ALA U 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 52 through 63 Processing helix chain 'W' and resid 64 through 75 Processing helix chain 'X' and resid 2 through 10 removed outlier: 3.659A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N SER X 10 " --> pdb=" O LEU X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 35 Processing helix chain 'X' and resid 40 through 61 removed outlier: 4.092A pdb=" N GLN X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 40 through 51 Processing helix chain 'Z' and resid 9 through 19 removed outlier: 5.100A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 8 through 15 Processing helix chain 'b' and resid 26 through 34 removed outlier: 4.183A pdb=" N ARG b 30 " --> pdb=" O ASN b 26 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N GLN b 31 " --> pdb=" O PRO b 27 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N TYR b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE b 34 " --> pdb=" O ARG b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 66 Proline residue: b 50 - end of helix Processing helix chain 'b' and resid 78 through 90 Processing helix chain 'b' and resid 105 through 126 removed outlier: 3.524A pdb=" N LEU b 109 " --> pdb=" O ASN b 105 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 132 through 150 Processing helix chain 'b' and resid 167 through 172 Processing helix chain 'b' and resid 173 through 182 Processing helix chain 'b' and resid 208 through 227 removed outlier: 4.319A pdb=" N LYS b 227 " --> pdb=" O ILE b 223 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 156 removed outlier: 4.262A pdb=" N ASN b 155 " --> pdb=" O GLY b 152 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.816A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU c 12 " --> pdb=" O ILE c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 48 removed outlier: 4.642A pdb=" N ALA c 30 " --> pdb=" O PRO c 26 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N GLU c 31 " --> pdb=" O LYS c 27 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 3.667A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 4.540A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 3.996A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 Processing helix chain 'c' and resid 129 through 145 Processing helix chain 'c' and resid 210 through 215 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.432A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 33 Processing helix chain 'd' and resid 51 through 68 Processing helix chain 'd' and resid 70 through 85 removed outlier: 5.111A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.774A pdb=" N ARG d 99 " --> pdb=" O LEU d 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 108 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 154 through 168 removed outlier: 4.224A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 removed outlier: 3.710A pdb=" N LEU d 193 " --> pdb=" O ASP d 189 " (cutoff:3.500A) Proline residue: d 194 - end of helix No H-bonds generated for 'chain 'd' and resid 189 through 194' Processing helix chain 'd' and resid 198 through 208 removed outlier: 4.321A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.055A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.620A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 157 Processing helix chain 'e' and resid 159 through 164 Processing helix chain 'f' and resid 11 through 19 removed outlier: 3.594A pdb=" N SER f 15 " --> pdb=" O HIS f 11 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N ASP f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N VAL f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 11 through 19' Processing helix chain 'f' and resid 20 through 33 Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 20 through 32 removed outlier: 5.589A pdb=" N GLN g 32 " --> pdb=" O ASN g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.679A pdb=" N LYS g 55 " --> pdb=" O GLN g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 111 Processing helix chain 'g' and resid 116 through 130 Processing helix chain 'g' and resid 132 through 149 Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 Processing helix chain 'h' and resid 113 through 121 Processing helix chain 'i' and resid 32 through 37 Processing helix chain 'i' and resid 39 through 54 removed outlier: 3.776A pdb=" N ARG i 43 " --> pdb=" O ARG i 39 " (cutoff:3.500A) Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 69 through 90 Processing helix chain 'i' and resid 91 through 100 removed outlier: 4.970A pdb=" N VAL i 95 " --> pdb=" O THR i 91 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.923A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 4.369A pdb=" N GLY k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 59 removed outlier: 5.175A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) Proline residue: k 59 - end of helix No H-bonds generated for 'chain 'k' and resid 53 through 59' Processing helix chain 'k' and resid 60 through 75 removed outlier: 4.271A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 4.173A pdb=" N VAL k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.649A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.106A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.756A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASP m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 4.078A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) Proline residue: m 64 - end of helix Processing helix chain 'm' and resid 66 through 84 removed outlier: 3.554A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 33 removed outlier: 5.163A pdb=" N ALA n 22 " --> pdb=" O ALA n 18 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N LYS n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 52 Proline residue: n 52 - end of helix Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.720A pdb=" N ASP n 86 " --> pdb=" O ASN n 82 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 3.500A pdb=" N GLN o 40 " --> pdb=" O ILE o 36 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.935A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 71 through 82 Processing helix chain 'p' and resid 86 through 100 Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.595A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 Processing helix chain 'r' and resid 48 through 66 Processing helix chain 's' and resid 12 through 26 removed outlier: 4.007A pdb=" N ASN s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.488A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 42 removed outlier: 3.603A pdb=" N VAL t 28 " --> pdb=" O LEU t 24 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 65 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 87 removed outlier: 3.770A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA t 87 " --> pdb=" O VAL t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 Processing helix chain 'u' and resid 28 through 37 removed outlier: 3.585A pdb=" N ARG u 35 " --> pdb=" O ASP u 31 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU u 36 " --> pdb=" O VAL u 32 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 64 Processing sheet with id= 1, first strand: chain '0' and resid 15 through 20 removed outlier: 6.266A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE 0 44 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N MET 0 30 " --> pdb=" O GLU 0 47 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 21 through 24 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain '3' and resid 1 through 4 removed outlier: 4.673A pdb=" N GLN 3 4 " --> pdb=" O ARG 3 36 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N SER 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 2 through 6 removed outlier: 6.542A pdb=" N VAL C 20 " --> pdb=" O PRO C 2 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N VAL C 16 " --> pdb=" O CYS C 6 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.852A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N SER C 118 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 165 through 168 removed outlier: 3.924A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.318A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 13.512A pdb=" N GLY D 201 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 11.776A pdb=" N LYS D 117 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N GLU D 171 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 37 through 41 removed outlier: 3.598A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU D 41 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR D 46 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLY D 97 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 10, first strand: chain 'D' and resid 25 through 29 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'D' and resid 47 through 52 removed outlier: 4.862A pdb=" N GLN D 47 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 107 through 110 removed outlier: 4.429A pdb=" N GLN D 108 " --> pdb=" O ILE D 180 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.542A pdb=" N SER E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 43 through 46 No H-bonds generated for sheet with id= 14 Processing sheet with id= 15, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.803A pdb=" N LYS E 184 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASP E 167 " --> pdb=" O ALA E 145 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 32 through 38 Processing sheet with id= 17, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 18, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 19, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.340A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 21, first strand: chain 'H' and resid 16 through 20 removed outlier: 6.697A pdb=" N ASP H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.548A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.149A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ASP J 81 " --> pdb=" O LYS J 66 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS J 66 " --> pdb=" O ASP J 81 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 68 through 71 removed outlier: 3.903A pdb=" N SER J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'L' and resid 38 through 41 No H-bonds generated for sheet with id= 25 Processing sheet with id= 26, first strand: chain 'L' and resid 63 through 66 removed outlier: 3.673A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE L 32 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE L 34 " --> pdb=" O LEU L 103 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS L 101 " --> pdb=" O ALA L 36 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'L' and resid 31 through 37 removed outlier: 7.349A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LYS L 128 " --> pdb=" O THR L 37 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 33 through 37 Processing sheet with id= 29, first strand: chain 'N' and resid 50 through 53 removed outlier: 3.523A pdb=" N ALA N 50 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL N 29 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 41 through 48 removed outlier: 6.721A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'O' and resid 52 through 55 removed outlier: 3.840A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 11 through 15 removed outlier: 4.033A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 17 through 21 removed outlier: 4.060A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 35, first strand: chain 'Q' and resid 65 through 74 removed outlier: 3.763A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N GLN Q 91 " --> pdb=" O HIS Q 69 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS Q 71 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS Q 89 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ARG Q 73 " --> pdb=" O GLN Q 87 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLN Q 87 " --> pdb=" O ARG Q 73 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 2 through 8 removed outlier: 4.746A pdb=" N THR R 100 " --> pdb=" O GLY R 79 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 28 through 32 removed outlier: 4.498A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 38 through 44 removed outlier: 5.458A pdb=" N ASN T 38 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'T' and resid 82 through 85 Processing sheet with id= 40, first strand: chain 'U' and resid 73 through 76 removed outlier: 3.522A pdb=" N HIS U 92 " --> pdb=" O GLN U 82 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 29 through 32 removed outlier: 4.721A pdb=" N GLN V 29 " --> pdb=" O VAL V 67 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL V 82 " --> pdb=" O GLY V 48 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 51 through 54 removed outlier: 4.358A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.342A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'W' and resid 34 through 41 Processing sheet with id= 45, first strand: chain 'Y' and resid 32 through 38 removed outlier: 4.447A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Z' and resid 28 through 31 removed outlier: 3.881A pdb=" N GLU Z 35 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 92 through 95 removed outlier: 3.779A pdb=" N ILE b 166 " --> pdb=" O VAL b 72 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 54 through 59 removed outlier: 3.805A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 164 through 170 removed outlier: 6.144A pdb=" N ASP c 181 " --> pdb=" O ARG c 204 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'd' and resid 143 through 146 removed outlier: 3.930A pdb=" N ASP d 143 " --> pdb=" O PHE d 184 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 11 through 15 removed outlier: 6.740A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA e 16 " --> pdb=" O LEU e 35 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.927A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 32 through 39 Processing sheet with id= 54, first strand: chain 'f' and resid 38 through 42 removed outlier: 6.136A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.600A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'g' and resid 73 through 77 Processing sheet with id= 57, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.512A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'h' and resid 75 through 78 removed outlier: 4.764A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'i' and resid 3 through 9 Processing sheet with id= 60, first strand: chain 'i' and resid 24 through 28 removed outlier: 3.961A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'j' and resid 35 through 38 removed outlier: 3.520A pdb=" N GLN j 35 " --> pdb=" O VAL j 77 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'j' and resid 42 through 53 removed outlier: 4.891A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) removed outlier: 8.491A pdb=" N ALA j 61 " --> pdb=" O THR j 53 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'k' and resid 28 through 35 removed outlier: 3.863A pdb=" N ASN k 28 " --> pdb=" O SER k 25 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY k 18 " --> pdb=" O ASN k 80 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'l' and resid 29 through 33 removed outlier: 5.118A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'l' and resid 35 through 41 removed outlier: 4.944A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'p' and resid 22 through 28 removed outlier: 3.622A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 8 through 12 removed outlier: 7.049A pdb=" N THR q 61 " --> pdb=" O VAL q 77 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ALA q 73 " --> pdb=" O SER q 65 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 20 through 32 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 's' and resid 47 through 52 removed outlier: 4.422A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) 1870 hydrogen bonds defined for protein. 5529 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3572 hydrogen bonds 5614 hydrogen bond angles 0 basepair planarities 1426 basepair parallelities 2119 stacking parallelities Total time for adding SS restraints: 292.53 Time building geometry restraints manager: 58.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 13140 1.31 - 1.44: 65790 1.44 - 1.56: 60803 1.56 - 1.69: 8770 1.69 - 1.81: 251 Bond restraints: 148754 Sorted by residual: bond pdb=" C14 YQM A3202 " pdb=" C15 YQM A3202 " ideal model delta sigma weight residual 1.035 1.577 -0.542 2.00e-02 2.50e+03 7.36e+02 bond pdb=" C14 YQM A3201 " pdb=" C15 YQM A3201 " ideal model delta sigma weight residual 1.035 1.572 -0.537 2.00e-02 2.50e+03 7.20e+02 bond pdb=" C14 YQM a1601 " pdb=" C15 YQM a1601 " ideal model delta sigma weight residual 1.035 1.566 -0.531 2.00e-02 2.50e+03 7.04e+02 bond pdb=" C08 YQM A3202 " pdb=" C09 YQM A3202 " ideal model delta sigma weight residual 1.951 1.546 0.405 2.00e-02 2.50e+03 4.09e+02 bond pdb=" C08 YQM A3201 " pdb=" C09 YQM A3201 " ideal model delta sigma weight residual 1.951 1.549 0.402 2.00e-02 2.50e+03 4.03e+02 ... (remaining 148749 not shown) Histogram of bond angle deviations from ideal: 88.24 - 99.80: 4 99.80 - 111.35: 92346 111.35 - 122.90: 104020 122.90 - 134.45: 26136 134.45 - 146.00: 6 Bond angle restraints: 222512 Sorted by residual: angle pdb=" N PRO m 115 " pdb=" CD PRO m 115 " pdb=" CG PRO m 115 " ideal model delta sigma weight residual 103.20 88.24 14.96 1.50e+00 4.44e-01 9.94e+01 angle pdb=" C1' G7M A2065 " pdb=" N9 G7M A2065 " pdb=" C8 G7M A2065 " ideal model delta sigma weight residual 94.96 122.29 -27.33 3.00e+00 1.11e-01 8.30e+01 angle pdb=" C1' G7M a 524 " pdb=" N9 G7M a 524 " pdb=" C8 G7M a 524 " ideal model delta sigma weight residual 94.96 121.39 -26.43 3.00e+00 1.11e-01 7.76e+01 angle pdb=" CA PRO m 115 " pdb=" N PRO m 115 " pdb=" CD PRO m 115 " ideal model delta sigma weight residual 112.00 101.77 10.23 1.40e+00 5.10e-01 5.34e+01 angle pdb=" C1' 6MZ A2026 " pdb=" N9 6MZ A2026 " pdb=" C8 6MZ A2026 " ideal model delta sigma weight residual 126.23 146.00 -19.77 3.00e+00 1.11e-01 4.34e+01 ... (remaining 222507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 76745 35.98 - 71.96: 2346 71.96 - 107.94: 212 107.94 - 143.91: 33 143.91 - 179.89: 71 Dihedral angle restraints: 79407 sinusoidal: 63700 harmonic: 15707 Sorted by residual: dihedral pdb=" O4' C a1448 " pdb=" C1' C a1448 " pdb=" N1 C a1448 " pdb=" C2 C a1448 " ideal model delta sinusoidal sigma weight residual -160.00 19.75 -179.75 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A2473 " pdb=" C1' U A2473 " pdb=" N1 U A2473 " pdb=" C2 U A2473 " ideal model delta sinusoidal sigma weight residual -160.00 16.42 -176.42 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A 912 " pdb=" C1' C A 912 " pdb=" N1 C A 912 " pdb=" C2 C A 912 " ideal model delta sinusoidal sigma weight residual 200.00 31.53 168.47 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 79404 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 27414 0.082 - 0.164: 975 0.164 - 0.246: 23 0.246 - 0.328: 7 0.328 - 0.410: 5 Chirality restraints: 28424 Sorted by residual: chirality pdb=" C05 YQM A3201 " pdb=" C04 YQM A3201 " pdb=" C06 YQM A3201 " pdb=" C19 YQM A3201 " both_signs ideal model delta sigma weight residual False 2.36 2.77 -0.41 2.00e-01 2.50e+01 4.20e+00 chirality pdb=" C05 YQM a1601 " pdb=" C04 YQM a1601 " pdb=" C06 YQM a1601 " pdb=" C19 YQM a1601 " both_signs ideal model delta sigma weight residual False 2.36 2.76 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" C05 YQM A3202 " pdb=" C04 YQM A3202 " pdb=" C06 YQM A3202 " pdb=" C19 YQM A3202 " both_signs ideal model delta sigma weight residual False 2.36 2.76 -0.40 2.00e-01 2.50e+01 3.94e+00 ... (remaining 28421 not shown) Planarity restraints: 11959 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2247 " 0.040 2.00e-02 2.50e+03 5.77e-01 7.49e+03 pdb=" C4' OMG A2247 " 0.435 2.00e-02 2.50e+03 pdb=" O4' OMG A2247 " 0.631 2.00e-02 2.50e+03 pdb=" C3' OMG A2247 " -0.590 2.00e-02 2.50e+03 pdb=" O3' OMG A2247 " -0.583 2.00e-02 2.50e+03 pdb=" C2' OMG A2247 " -0.203 2.00e-02 2.50e+03 pdb=" O2' OMG A2247 " 0.923 2.00e-02 2.50e+03 pdb=" C1' OMG A2247 " 0.226 2.00e-02 2.50e+03 pdb=" N9 OMG A2247 " -0.880 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A2441 " -0.031 2.00e-02 2.50e+03 5.73e-01 7.40e+03 pdb=" C4' 2MG A2441 " -0.437 2.00e-02 2.50e+03 pdb=" O4' 2MG A2441 " -0.646 2.00e-02 2.50e+03 pdb=" C3' 2MG A2441 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG A2441 " 0.568 2.00e-02 2.50e+03 pdb=" C2' 2MG A2441 " 0.213 2.00e-02 2.50e+03 pdb=" O2' 2MG A2441 " -0.904 2.00e-02 2.50e+03 pdb=" C1' 2MG A2441 " -0.226 2.00e-02 2.50e+03 pdb=" N9 2MG A2441 " 0.875 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1204 " 0.037 2.00e-02 2.50e+03 5.67e-01 7.23e+03 pdb=" C4' 2MG a1204 " 0.432 2.00e-02 2.50e+03 pdb=" O4' 2MG a1204 " 0.616 2.00e-02 2.50e+03 pdb=" C3' 2MG a1204 " -0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG a1204 " -0.566 2.00e-02 2.50e+03 pdb=" C2' 2MG a1204 " -0.211 2.00e-02 2.50e+03 pdb=" O2' 2MG a1204 " 0.909 2.00e-02 2.50e+03 pdb=" C1' 2MG a1204 " 0.229 2.00e-02 2.50e+03 pdb=" N9 2MG a1204 " -0.857 2.00e-02 2.50e+03 ... (remaining 11956 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 919 2.39 - 3.02: 70972 3.02 - 3.64: 237057 3.64 - 4.27: 397457 4.27 - 4.90: 531344 Nonbonded interactions: 1237749 Sorted by model distance: nonbonded pdb=" O2' G a 85 " pdb=" OP2 C a 86 " model vdw 1.760 2.440 nonbonded pdb="MG MG a1635 " pdb=" O HOH a1744 " model vdw 1.802 2.170 nonbonded pdb=" O2' A a 789 " pdb=" OP2 U a 790 " model vdw 1.808 2.440 nonbonded pdb="MG MG a1644 " pdb=" O HOH a1718 " model vdw 1.822 2.170 nonbonded pdb="MG MG a1635 " pdb=" O HOH a1740 " model vdw 1.828 2.170 ... (remaining 1237744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.580 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.600 Construct map_model_manager: 0.130 Extract box with map and model: 30.280 Check model and map are aligned: 1.490 Set scattering table: 1.000 Process input model: 568.890 Find NCS groups from input model: 2.610 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 623.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.542 148754 Z= 0.362 Angle : 0.554 27.334 222512 Z= 0.291 Chirality : 0.034 0.410 28424 Planarity : 0.013 0.577 11959 Dihedral : 14.989 179.892 69289 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.82 % Favored : 96.97 % Rotamer: Outliers : 0.02 % Allowed : 0.07 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.11), residues: 5420 helix: 2.32 (0.12), residues: 1873 sheet: 0.82 (0.16), residues: 1075 loop : -0.09 (0.12), residues: 2472 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1114 time to evaluate : 6.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 2 residues processed: 1114 average time/residue: 2.3175 time to fit residues: 3586.7787 Evaluate side-chains 1003 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1001 time to evaluate : 5.846 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 1.4376 time to fit residues: 10.9546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 817 optimal weight: 10.0000 chunk 733 optimal weight: 8.9990 chunk 407 optimal weight: 7.9990 chunk 250 optimal weight: 9.9990 chunk 494 optimal weight: 9.9990 chunk 391 optimal weight: 40.0000 chunk 758 optimal weight: 20.0000 chunk 293 optimal weight: 30.0000 chunk 461 optimal weight: 3.9990 chunk 564 optimal weight: 5.9990 chunk 879 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN C 61 HIS C 120 ASN D 129 ASN D 137 HIS E 29 GLN I 12 GLN I 61 GLN M 23 ASN M 62 ASN O 15 GLN O 55 ASN Q 6 GLN S 58 ASN V 12 ASN V 35 ASN W 17 ASN W 36 HIS ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 87 GLN b 111 GLN c 123 GLN c 140 ASN ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 120 HIS f 3 HIS g 21 GLN h 18 GLN h 38 ASN h 42 GLN i 73 GLN i 98 GLN k 21 HIS k 27 ASN ** k 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 72 HIS m 28 HIS n 90 GLN o 40 GLN o 62 GLN t 14 ASN u 43 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.134 148754 Z= 0.643 Angle : 1.098 20.416 222512 Z= 0.540 Chirality : 0.059 0.528 28424 Planarity : 0.009 0.145 11959 Dihedral : 15.655 179.716 58537 Min Nonbonded Distance : 1.569 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.32 % Favored : 96.44 % Rotamer: Outliers : 3.45 % Allowed : 10.60 % Favored : 85.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.11), residues: 5420 helix: 1.11 (0.11), residues: 1865 sheet: 0.57 (0.16), residues: 1045 loop : -0.60 (0.11), residues: 2510 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 1010 time to evaluate : 5.815 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 155 outliers final: 87 residues processed: 1068 average time/residue: 2.2742 time to fit residues: 3375.7461 Evaluate side-chains 1062 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 975 time to evaluate : 5.873 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 47 residues processed: 42 average time/residue: 1.3794 time to fit residues: 101.8303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 488 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 731 optimal weight: 5.9990 chunk 598 optimal weight: 1.9990 chunk 242 optimal weight: 6.9990 chunk 880 optimal weight: 5.9990 chunk 951 optimal weight: 0.9980 chunk 784 optimal weight: 10.0000 chunk 873 optimal weight: 1.9990 chunk 300 optimal weight: 7.9990 chunk 706 optimal weight: 0.5980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN C 61 HIS C 120 ASN D 129 ASN E 29 GLN I 61 GLN J 29 HIS M 23 ASN M 62 ASN O 9 GLN ** O 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 ASN V 35 ASN b 111 GLN d 44 GLN d 50 GLN h 18 GLN h 38 ASN h 42 GLN i 73 GLN i 98 GLN j 56 HIS k 27 ASN l 72 HIS n 90 GLN o 40 GLN t 14 ASN u 43 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 148754 Z= 0.242 Angle : 0.688 16.158 222512 Z= 0.365 Chirality : 0.040 0.395 28424 Planarity : 0.006 0.130 11959 Dihedral : 15.172 179.733 58537 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.18 % Allowed : 2.60 % Favored : 97.21 % Rotamer: Outliers : 3.52 % Allowed : 13.23 % Favored : 83.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.11), residues: 5420 helix: 1.61 (0.12), residues: 1870 sheet: 0.61 (0.15), residues: 1082 loop : -0.52 (0.12), residues: 2468 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1180 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 1022 time to evaluate : 6.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 158 outliers final: 86 residues processed: 1085 average time/residue: 2.3084 time to fit residues: 3486.1327 Evaluate side-chains 1079 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 993 time to evaluate : 5.911 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 47 residues processed: 41 average time/residue: 1.2608 time to fit residues: 96.0396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 870 optimal weight: 2.9990 chunk 662 optimal weight: 5.9990 chunk 457 optimal weight: 0.9980 chunk 97 optimal weight: 8.9990 chunk 420 optimal weight: 7.9990 chunk 591 optimal weight: 5.9990 chunk 883 optimal weight: 9.9990 chunk 935 optimal weight: 0.9990 chunk 461 optimal weight: 1.9990 chunk 837 optimal weight: 7.9990 chunk 252 optimal weight: 9.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN C 61 HIS C 120 ASN C 260 ASN D 129 ASN I 61 GLN J 29 HIS M 23 ASN M 62 ASN N 66 ASN ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN S 29 GLN V 12 ASN V 35 ASN ** b 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 111 GLN ** c 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 GLN d 50 GLN ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 GLN h 38 ASN h 41 GLN h 42 GLN i 73 GLN i 98 GLN k 23 HIS k 27 ASN n 90 GLN o 40 GLN o 62 GLN t 14 ASN u 43 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 148754 Z= 0.274 Angle : 0.719 18.803 222512 Z= 0.377 Chirality : 0.041 0.412 28424 Planarity : 0.006 0.131 11959 Dihedral : 15.149 179.669 58537 Min Nonbonded Distance : 1.706 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.23 % Favored : 96.62 % Rotamer: Outliers : 3.79 % Allowed : 14.30 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.11), residues: 5420 helix: 1.62 (0.12), residues: 1863 sheet: 0.59 (0.16), residues: 1073 loop : -0.56 (0.12), residues: 2484 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1004 time to evaluate : 5.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 170 outliers final: 96 residues processed: 1076 average time/residue: 2.3130 time to fit residues: 3469.1664 Evaluate side-chains 1083 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 987 time to evaluate : 5.871 Switching outliers to nearest non-outliers outliers start: 96 outliers final: 56 residues processed: 42 average time/residue: 1.3143 time to fit residues: 99.4586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 779 optimal weight: 2.9990 chunk 531 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 696 optimal weight: 3.9990 chunk 386 optimal weight: 10.0000 chunk 798 optimal weight: 0.8980 chunk 646 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 477 optimal weight: 10.0000 chunk 839 optimal weight: 5.9990 chunk 236 optimal weight: 8.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN C 61 HIS C 120 ASN C 260 ASN D 129 ASN I 61 GLN J 29 HIS M 23 ASN M 62 ASN ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN V 12 ASN V 35 ASN b 91 GLN b 111 GLN ** c 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 GLN d 50 GLN ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 GLN h 38 ASN h 42 GLN i 73 GLN i 98 GLN k 27 ASN n 90 GLN o 40 GLN o 62 GLN t 14 ASN u 43 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 148754 Z= 0.359 Angle : 0.803 19.511 222512 Z= 0.415 Chirality : 0.045 0.436 28424 Planarity : 0.007 0.134 11959 Dihedral : 15.296 179.924 58537 Min Nonbonded Distance : 1.670 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.27 % Favored : 96.57 % Rotamer: Outliers : 4.05 % Allowed : 15.33 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.11), residues: 5420 helix: 1.37 (0.12), residues: 1869 sheet: 0.47 (0.15), residues: 1078 loop : -0.68 (0.11), residues: 2473 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 964 time to evaluate : 5.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 182 outliers final: 112 residues processed: 1047 average time/residue: 2.3387 time to fit residues: 3437.9960 Evaluate side-chains 1064 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 952 time to evaluate : 5.801 Switching outliers to nearest non-outliers outliers start: 112 outliers final: 64 residues processed: 50 average time/residue: 1.3412 time to fit residues: 116.6523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 314 optimal weight: 0.0000 chunk 842 optimal weight: 0.9980 chunk 184 optimal weight: 10.0000 chunk 549 optimal weight: 0.8980 chunk 230 optimal weight: 10.0000 chunk 936 optimal weight: 7.9990 chunk 777 optimal weight: 0.7980 chunk 433 optimal weight: 0.9990 chunk 77 optimal weight: 9.9990 chunk 309 optimal weight: 5.9990 chunk 491 optimal weight: 4.9990 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN C 61 HIS C 120 ASN C 260 ASN D 129 ASN G 74 ASN I 61 GLN J 29 HIS J 59 ASN M 23 ASN M 62 ASN O 9 GLN O 55 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN V 12 ASN W 23 ASN b 111 GLN c 49 ASN ** c 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 GLN d 50 GLN ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 GLN h 38 ASN i 73 GLN i 98 GLN k 27 ASN o 40 GLN o 62 GLN s 83 HIS t 14 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 148754 Z= 0.131 Angle : 0.579 14.368 222512 Z= 0.313 Chirality : 0.035 0.388 28424 Planarity : 0.005 0.121 11959 Dihedral : 14.895 179.979 58537 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.75 % Favored : 97.10 % Rotamer: Outliers : 2.72 % Allowed : 17.55 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.11), residues: 5420 helix: 1.95 (0.12), residues: 1865 sheet: 0.66 (0.16), residues: 1077 loop : -0.48 (0.12), residues: 2478 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 997 time to evaluate : 6.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 79 residues processed: 1067 average time/residue: 2.2792 time to fit residues: 3394.2436 Evaluate side-chains 1046 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 967 time to evaluate : 5.210 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 65 residues processed: 17 average time/residue: 1.2087 time to fit residues: 41.7101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 902 optimal weight: 3.9990 chunk 105 optimal weight: 10.0000 chunk 533 optimal weight: 0.9980 chunk 683 optimal weight: 3.9990 chunk 529 optimal weight: 9.9990 chunk 788 optimal weight: 9.9990 chunk 522 optimal weight: 1.9990 chunk 932 optimal weight: 3.9990 chunk 583 optimal weight: 4.9990 chunk 568 optimal weight: 9.9990 chunk 430 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN C 61 HIS C 120 ASN D 129 ASN I 61 GLN J 29 HIS M 23 ASN ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN V 12 ASN b 111 GLN ** c 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 GLN h 18 GLN h 38 ASN h 42 GLN i 73 GLN i 98 GLN n 90 GLN o 40 GLN o 62 GLN t 14 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 148754 Z= 0.304 Angle : 0.735 15.885 222512 Z= 0.383 Chirality : 0.042 0.424 28424 Planarity : 0.006 0.129 11959 Dihedral : 15.077 179.927 58537 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.36 % Favored : 96.51 % Rotamer: Outliers : 3.14 % Allowed : 17.46 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.11), residues: 5420 helix: 1.66 (0.12), residues: 1874 sheet: 0.57 (0.16), residues: 1080 loop : -0.58 (0.12), residues: 2466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 972 time to evaluate : 5.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 141 outliers final: 99 residues processed: 1042 average time/residue: 2.2818 time to fit residues: 3320.5443 Evaluate side-chains 1070 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 971 time to evaluate : 5.797 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 59 residues processed: 41 average time/residue: 1.5437 time to fit residues: 108.6489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 577 optimal weight: 3.9990 chunk 372 optimal weight: 30.0000 chunk 557 optimal weight: 6.9990 chunk 281 optimal weight: 10.0000 chunk 183 optimal weight: 20.0000 chunk 180 optimal weight: 10.0000 chunk 593 optimal weight: 50.0000 chunk 635 optimal weight: 6.9990 chunk 461 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 733 optimal weight: 8.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN C 61 HIS C 86 ASN C 120 ASN C 260 ASN D 129 ASN I 61 GLN J 29 HIS M 23 ASN M 62 ASN ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 111 GLN ** c 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 123 GLN d 44 GLN ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 GLN h 38 ASN h 42 GLN i 73 GLN i 98 GLN n 90 GLN o 40 GLN o 62 GLN t 14 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.112 148754 Z= 0.541 Angle : 0.989 25.844 222512 Z= 0.493 Chirality : 0.054 0.487 28424 Planarity : 0.008 0.139 11959 Dihedral : 15.502 179.494 58537 Min Nonbonded Distance : 1.588 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.54 % Favored : 96.27 % Rotamer: Outliers : 3.36 % Allowed : 17.84 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.11), residues: 5420 helix: 1.08 (0.12), residues: 1866 sheet: 0.35 (0.15), residues: 1089 loop : -0.83 (0.11), residues: 2465 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 964 time to evaluate : 6.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 151 outliers final: 106 residues processed: 1049 average time/residue: 2.2811 time to fit residues: 3338.0503 Evaluate side-chains 1065 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 959 time to evaluate : 5.829 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 71 residues processed: 36 average time/residue: 1.3581 time to fit residues: 88.0743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 848 optimal weight: 5.9990 chunk 893 optimal weight: 1.9990 chunk 815 optimal weight: 2.9990 chunk 869 optimal weight: 0.7980 chunk 523 optimal weight: 7.9990 chunk 378 optimal weight: 7.9990 chunk 682 optimal weight: 0.5980 chunk 266 optimal weight: 10.0000 chunk 785 optimal weight: 0.8980 chunk 822 optimal weight: 0.9980 chunk 866 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN C 61 HIS C 120 ASN C 260 ASN D 129 ASN I 61 GLN J 29 HIS M 23 ASN M 62 ASN O 9 GLN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 ASN b 111 GLN ** c 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 GLN d 118 GLN h 18 GLN ** h 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN i 73 GLN i 98 GLN n 90 GLN o 40 GLN t 14 ASN t 82 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7254 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.097 148754 Z= 0.136 Angle : 0.597 14.547 222512 Z= 0.322 Chirality : 0.036 0.380 28424 Planarity : 0.005 0.120 11959 Dihedral : 14.903 179.893 58537 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.66 % Favored : 97.21 % Rotamer: Outliers : 2.27 % Allowed : 19.31 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.11), residues: 5420 helix: 1.83 (0.12), residues: 1864 sheet: 0.50 (0.15), residues: 1117 loop : -0.57 (0.12), residues: 2439 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 996 time to evaluate : 5.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 78 residues processed: 1068 average time/residue: 2.2534 time to fit residues: 3375.6068 Evaluate side-chains 1064 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 986 time to evaluate : 5.824 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 62 residues processed: 18 average time/residue: 1.0988 time to fit residues: 42.0456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 570 optimal weight: 8.9990 chunk 919 optimal weight: 7.9990 chunk 561 optimal weight: 0.8980 chunk 436 optimal weight: 2.9990 chunk 639 optimal weight: 5.9990 chunk 964 optimal weight: 20.0000 chunk 887 optimal weight: 2.9990 chunk 767 optimal weight: 0.8980 chunk 79 optimal weight: 9.9990 chunk 593 optimal weight: 50.0000 chunk 470 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN C 61 HIS C 120 ASN C 260 ASN D 129 ASN I 61 GLN J 29 HIS M 23 ASN ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 37 ASN V 12 ASN ** c 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 GLN f 46 GLN h 18 GLN h 38 ASN h 42 GLN i 73 GLN i 98 GLN n 90 GLN o 40 GLN o 62 GLN p 81 GLN t 14 ASN t 82 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7330 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 148754 Z= 0.287 Angle : 0.719 15.421 222512 Z= 0.376 Chirality : 0.041 0.407 28424 Planarity : 0.006 0.129 11959 Dihedral : 15.021 179.750 58537 Min Nonbonded Distance : 1.704 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.32 % Favored : 96.57 % Rotamer: Outliers : 2.14 % Allowed : 19.58 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.11), residues: 5420 helix: 1.66 (0.12), residues: 1867 sheet: 0.54 (0.16), residues: 1074 loop : -0.63 (0.12), residues: 2479 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10840 Ramachandran restraints generated. 5420 Oldfield, 0 Emsley, 5420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1064 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 968 time to evaluate : 5.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 96 outliers final: 78 residues processed: 1034 average time/residue: 2.3216 time to fit residues: 3353.1228 Evaluate side-chains 1041 residues out of total 4489 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 963 time to evaluate : 5.845 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 63 residues processed: 16 average time/residue: 1.4385 time to fit residues: 43.9526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 609 optimal weight: 8.9990 chunk 818 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 chunk 708 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 chunk 769 optimal weight: 1.9990 chunk 321 optimal weight: 10.0000 chunk 789 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 141 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 42 GLN C 61 HIS C 120 ASN C 260 ASN D 129 ASN I 61 GLN J 29 HIS L 3 GLN M 23 ASN M 62 ASN ** O 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 ASN ** Q 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 26 ASN ** c 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 123 GLN d 44 GLN ** d 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 GLN h 42 GLN i 73 GLN n 90 GLN o 40 GLN o 62 GLN t 14 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.149366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.136638 restraints weight = 158418.242| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 0.59 r_work: 0.3406 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.106 148754 Z= 0.507 Angle : 0.953 21.335 222512 Z= 0.478 Chirality : 0.052 0.478 28424 Planarity : 0.008 0.137 11959 Dihedral : 15.400 179.549 58537 Min Nonbonded Distance : 1.593 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.73 % Favored : 96.11 % Rotamer: Outliers : 2.34 % Allowed : 19.67 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.11), residues: 5420 helix: 1.11 (0.12), residues: 1870 sheet: 0.32 (0.15), residues: 1097 loop : -0.83 (0.11), residues: 2453 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 45844.96 seconds wall clock time: 792 minutes 55.57 seconds (47575.57 seconds total)